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feat(models): make pygam an optional dependency - #1381
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Every pyGAM release caps scipy<1.17 (dswah/pyGAM#584), so a required pygam holds scipy back for all CellRank users and fails to solve where scipy is pinned by conda. Only cellrank.models.GAM needs it: import it lazily there and point to `pip install cellrank[gam]` when it is missing. Co-Authored-By: Claude Opus 5.5 <[email protected]>
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Summary
pygammoves fromdependenciesto a newgamextra.cellrank.models.GAMimports it lazily and raisesModuleNotFoundErrorwithpip install cellrank[gam]when it is missing;import cellrankno longer needs it.pygamjoins thetestgroup;docs/installation.mdandAGENTS.mdlist the extra.Why
Every pyGAM release (0.10.1–0.12.0) declares
scipy<1.17(dswah/pyGAM#584, open since May). As a required dependency it holds pip users on scipy 1.16 and makes CellRank unsolvable wherever scipy is pinned by conda (e.g. pixi with conda-forge scipy 1.18). OnlyGAMuses it.Breaking change
Fitting gene trends with
cr.models.GAMnow needspip install "cellrank[gam]"— worth a line in the release notes. The conda-forge recipe can keep pygam as a run dependency (conda-forge's pygam has no scipy cap).Testing
tests/test_model.py,tests/test_utils.py: 272 passed, 14 skipped (Python 3.12, scipy 1.16.3, pygam 0.12.0).import cellrankwith pygam blocked (subprocess), andGAM()raising the install hint.PETSc / SLEPc + Rjob has failed onmainsince 2026-10-01 (petsc4py 3.26 removedMat.getVecs); unrelated, follow-up PR.🤖 Generated with Claude Code